Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_018372539.1 BN415_RS01710 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH8 (254 letters) >NCBI__GCF_000341525.1:WP_018372539.1 Length = 511 Score = 126 bits (316), Expect = 1e-33 Identities = 74/229 (32%), Positives = 128/229 (55%), Gaps = 13/229 (5%) Query: 3 LLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTL 62 ++E++ +TK FG A + L L GE+ L+G NGAGK+TL N+L G+ EP+ G + + Sbjct: 6 VIEMRDITKIFGEFVANDKINLHLRRGEIHALLGENGAGKSTLMNMLAGLLEPTSGEIVV 65 Query: 63 DGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFY 122 +G + SP K A+LG+G Q+ L + TV +N+++ G+ +H Sbjct: 66 NGKTVQLDSPSKAAALGIGMVHQHFMLVEAFTVAENIIL--GSETTKHGVLD------IK 117 Query: 123 KSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGM 182 K+ +E+K EL + + L D +++S G Q+R+EI++ L IL DEP A + Sbjct: 118 KATQEIK----ELSEKYGLAVDPSAKVEDISVGAQQRVEILKTLYRGADILIFDEPTAVL 173 Query: 183 NPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLI 231 P E EL ++++ + E K +++LI H ++ + V +R+ V+ G+ I Sbjct: 174 TPSEIEELEKIMKNLVKEGK-SLILITHKLDEIRAVADRVTVIRRGKSI 221 Score = 84.0 bits (206), Expect = 6e-21 Identities = 62/255 (24%), Positives = 135/255 (52%), Gaps = 16/255 (6%) Query: 3 LLEVKQLTKHFG-GLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVT 61 +L +K L + G+ AV ++L++ GE+VG+ G +G G++ L +TG+ + EGT+T Sbjct: 258 ILSIKDLVVNENRGIPAVKGLSLDVRAGEIVGIAGIDGNGQSELVQAITGLRKVKEGTIT 317 Query: 62 LDGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVL---IAFGNHHKQHVFTSFLRL 118 + G + G SP KI + + ++ +D VLD ++ IA ++K+ + + + Sbjct: 318 IKGENVVGHSPRKITEMQVSHVPED--RHRDGLVLDMMISENIALQTYYKEPLSKNGI-- 373 Query: 119 PAFYKSEKELKAKALELLKIFDLDGDAETL-AKNLSYGQQRRLEIVRALATEPKILFLDE 177 + + + A +L+K FD+ +E + A LS G Q++ + R + P +L + + Sbjct: 374 ----LNYNNITSYAKKLMKEFDVRAASEFVPASALSGGNQQKAIVAREIDRNPDLLIVSQ 429 Query: 178 PAAGMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPD 237 P G++ + + + +D+ K ++++ +++ ++ +++RI V+ G++ P+ Sbjct: 430 PTRGLDVGAIEYIHKRLIEERDKGK-AVLVVSFELDEILNLSDRIAVIHDGKIQGIVLPE 488 Query: 238 EIKTNKRVIEAYLGG 252 E TNK+ + + G Sbjct: 489 E--TNKQELGILMAG 501 Lambda K H 0.319 0.139 0.385 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 322 Number of extensions: 17 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 254 Length of database: 511 Length adjustment: 29 Effective length of query: 225 Effective length of database: 482 Effective search space: 108450 Effective search space used: 108450 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory